10 papers
Continuous-Time Quantum Walks based Graph Neural Network
Yuliang Zhan, Zefeng Gao, Jian Li +2
Graph Neural Networks (GNNs) are widely used on graph-structured data, but most suffer from two key weaknesses. First, message passing behaves as a low-pass filter under the homoph…
CARD: Coarse-to-fine Autoregressive Modeling with Radix-based Decomposition for Transferable Free Energy Estimation
Ziyang Yu, Yi He, Wenbing Huang +2
Estimating free energy differences quantifies thermodynamic preferences in molecular interactions, which is central to chemistry and drug discovery. Despite fruitful progress, exis…
UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules
Ziyang Yu, Wenbing Huang, Yang Liu
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However…
CloDS: Visual-Only Unsupervised Cloth Dynamics Learning in Unknown Conditions
Yuliang Zhan, Jian Li, Wenbing Huang +2
Deep learning has demonstrated remarkable capabilities in simulating complex dynamic systems. However, existing methods require known physical properties as supervision or inputs,…
Unified Biomolecular Trajectory Generation via Pretrained Variational Bridge
Ziyang Yu, Wenbing Huang, Yang Liu
Molecular Dynamics (MD) simulations provide a fundamental tool for characterizing molecular behavior at full atomic resolution, but their applicability is severely constrained by t…
Latent Retrieval Augmented Generation of Cross-Domain Protein Binders
Zishen Zhang, Xiangzhe Kong, Wenbing Huang +1
Designing protein binders targeting specific sites, which requires to generate realistic and functional interaction patterns, is a fundamental challenge in drug discovery. Current…